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Crystal structure of TAF3 phd finger bound to histone H3C4ME3 peptide

Analyse Crystal structure of TAF3 phd finger bound to histone H3C4ME3 peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5C13
Type: protein
Length: 260 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Transcription initiation factor tfiid subunit 3; H3 peptide
UniProt: Q5VWG9
Ligands: ZN
Pockets: 2 · best druggability 0.39

Structure

x-ray diffraction · 2 distinct chains · 6% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, E, G	Transcription initiation factor tfiid subunit 3	protein	59	7% helix, 22% strand	Q5VWG9
P, D, F, H	H3 peptide	protein	6	0% helix, 33% strand	—

Ligands and binding sites

ZN · Zinc ion · metal · 8 copies · chains A, C, E, G

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	91	0.39	0.77	18	empty
2	90	0.35	0.75	17	empty

Interfaces

10 interfaces between chains.

A–E · 538 Å² buried · 8 hydrogen bonds · protein-protein
C–G · 523 Å² buried · 7 hydrogen bonds · protein-protein
E–F · 479 Å² buried · 9 hydrogen bonds · protein-protein
A–P · 475 Å² buried · 9 hydrogen bonds · protein-protein
C–D · 472 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 modified (nonstandard).

Compared structures

5C13 · Crystal Structure of TAF3 PHD finger bound to histone H3C4me3 peptide · the same entry in another collection · chain H against H, TM-score 1.00
Q5VWG9 · AlphaFold monomer V2.0 prediction for transcription initiation factor tfiid subunit 3… · a predicted model of the same protein · chain A against A, TM-score 0.89

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q5VWG9
Elsewhere: RCSB PDB 5C13 · PDBe 5C13 · UniProt Q5VWG9

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